3OQN

Structure of ccpa-hpr-ser46-p-gntr-down cre


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.

Schumacher, M.A.Sprehe, M.Bartholomae, M.Hillen, W.Brennan, R.G.

(2011) Nucleic Acids Res 39: 2931-2942

  • DOI: https://doi.org/10.1093/nar/gkq1177
  • Primary Citation of Related Structures:  
    3OQM, 3OQN, 3OQO

  • PubMed Abstract: 

    In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR proteins, CcpA is activated for DNA binding by first forming a complex with the phosphoprotein HPr-Ser46-P. Bacillus subtilis CcpA functions as both a transcription repressor and activator and binds to more than 50 operators called catabolite response elements (cres). These sites are highly degenerate with the consensus, WTGNNARCGNWWWCAW. How CcpA-(HPr-Ser46-P) binds such diverse sequences is unclear. To gain insight into this question, we solved the structures of the CcpA-(HPr-Ser46-P) complex bound to three different operators, the synthetic (syn) cre, ackA2 cre and gntR-down cre. Strikingly, the structures show that the CcpA-bound operators display different bend angles, ranging from 31° to 56°. These differences are accommodated by a flexible linkage between the CcpA helix-turn-helix-loop-helix motif and hinge helices, which allows independent docking of these DNA-binding modules. This flexibility coupled with an abundance of non-polar residues capable of non-specific nucleobase interactions permits CcpA-(HPr-Ser46-P) to bind diverse operators. Indeed, biochemical data show that CcpA-(HPr-Ser46-P) binds the three cre sites with similar affinities. Thus, the data reveal properties that license this protein to function as a global transcription regulator.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. maschuma@mdanderson.org


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catabolite control protein A
A, C
339Bacillus subtilisMutation(s): 0 
Gene Names: alsAamyRBSU29740ccpAgraR
UniProt
Find proteins for P25144 (Bacillus subtilis (strain 168))
Explore P25144 
Go to UniProtKB:  P25144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25144
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphocarrier protein HPrB [auth S],
D
87Bacillus subtilisMutation(s): 0 
Gene Names: BSU13900hprptsH
EC: 2.7.11
UniProt
Find proteins for P08877 (Bacillus subtilis (strain 168))
Explore P08877 
Go to UniProtKB:  P08877
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UniProt GroupP08877
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*TP*AP*CP*CP*AP*T)-3'16Bacillus subtilis
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*GP*GP*TP*AP*CP*CP*GP*CP*TP*TP*TP*CP*AP*A)-3'F [auth B]16Bacillus subtilis
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B [auth S],
D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.93α = 90
b = 103.51β = 90
c = 175.34γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary